As the scale of high performance computer keeps increasing, the hierarchical high dimension direct network, such as Cray Dragonfly and K computer 6D mesh, becomes commonly used. In such architecture, the variety of topologies in each hierarchy leads to the complexity of topology and routing algorithm. Facing to the high complexity and scalability, parallel network simulator is the suitable platform to design network architecture efficiently and study its performance. We design and implement a packet-level parallel network simulator HiNetSim which can achieve both high accuracy and efficiency. In addition, the simulator provides flexible interfaces and configuration files for establishing hierarchical topologies and implementing routing algorithms. As a demonstration of HiNetSim, studies on flattened butterfly, 4D Torus and a proposed hierarchical network are given. Evaluation shows that HiNetSim achieves linear parallel speedup and is capable of simulating the network with tens of thousands nodes.